This study addresses challenges inherent to water quality monitoring devices used in aquaculture, especially in extensive pond systems. These challenges include vulnerability to contamination, complex maintenance requirements, and constrained monitoring scope. We introduce a design and implementation strategy for a water quality monitoring system that leverages unmanned aerial vehicles (UAVs) integrated with three-dimensional Geographic Information Systems (3D GIS). Utilizing 3D GIS technology facilitates the creation of a precise operational milieu for the aquaculture monitoring UAV. This includes defining virtual trajectories for safety zones and operational pathways, thereby mitigating the risk of UAV positional loss. Furthermore, on-site experiments were undertaken to quantify deviations from the designated virtual operational trajectory. Results suggest that the proposed UAV-centric water quality monitoring system, enhanced by 3D GIS, not only offers precision in positioning and stability during flight but also ensures dependable data acquisition and supports offline maintenance procedures. Moreover, this system is capable of servicing water expanses exceeding 1000 acres, remaining unaffected by the fragmentation patterns inherent to large pond systems.